This happened to me with Continental time and time again--always at Newark. Refunds, exchanges, whatever. It always manages to be messed up there.
I think my personal favorite was when the agent told me that my ticket was issued backwards in time (leaving in August, returning in July). Since I bought the ticket from Continental, I explained that this could have only been THEIR mistake.
I also called 800-WE-CARE-2, got scolded with a lecture about how airlines work, and then called reservations. No problem with the ticket whatsoever--it wasn't issued backwards in time at all. BUT, I missed my flight and had to stay overnight in Newark.
My sister is a devout Continental flyer, but I fail to see the light. I switched to Delta a few years ago and it's been great. I hate Atlanta and Delta doesn't have electronic check-in (yet), but they always appear to be MUCH more organized. And I've only encountered difficult employees a couple of times.
I don't understand how Continental has developed this great reputation. Yes, they've turned around, but I just think that they're less reliable and less organized than Delta.